By popular request here is my own shell script for remixing minecraft.jar files and packing in the plugins I prefer. I offer no support, no documentation (read the source so you know what it does! it's short), and only state truthfully that it works for me. If you can't figure out how this script works, you either need to learn more (man dash is a good place to start) or shouldn't run your own server (pay someone else to or join a community one).
Here's the script, I think it requires you have a working java installed (pack/unpack maybe, can't remember offhand) and know you need p7zip (often called p7zip-full) installed.
(c) MJEvans 2012, released here under GPLv3 (however it is mostly built out of facts and nothing prevents you from assembling your own collection of facts)
Please file any legitimate bug reports for this script under this thread.
(This does not include you being unable to get it to work at all, since I know it will work and getting the folder structure correct is an intentional lack of documentation to force you to look at how it works and understand what it's automating for you.)